Starfleet Intelligence is a branch of Starfleet responsible for gathering and analyzing information concerning neighboring powers in the galaxy, and for carrying out covert investigations regarding possible threats to Earth and, later, the Federation.
Starfleet Intelligence employed agents for their field operations, who were authorized to perform undercover investigations. Starfleet Intelligence agents (or “S.I. agents”) reported to Division Heads, who oversaw their agents’ missions. The head of the organization was known as the Chief of Starfleet Intelligence.
In 2154, Starfleet Intelligence was in possession of knowledge that the Klingons were maintaining a genetic research facility on Qu’Vat colony. This information would prove valuable to the crew of the Enterprise NX-01 when attempting to rescue Doctor Phlox, who had been abducted by the Klingons.
In 2155, S.I. agent Gannet Brooks, posing as a reporter, reconnected with Travis Mayweather, with whom she had previously been engaged in a relationship, in an attempt to gather intelligence on the xenophobic terrorist group Terra Prime. When Lieutenant Reed discovered that Gannet had reprogrammed her universal translator to secretly eavesdrop on the conversations of the Coalition of Planets delegates, the crew of Enterprise began to suspect that she herself was a spy for Terra Prime, and placed her in the brig. Gannet later confided in Mayweather that she worked for Starfleet Intelligence, telling him that she could not reveal her identity lest the actual Terra Prime operative find out. Mayweather, however, did not believe her, until it was revealed that Ensign Masaro was the real spy.
In 2268, Starfleet Intelligence reported that the Romulan military was using the Klingon D7 class battle cruiser design for the construction of their own starships.
In 2358, Starfleet Intelligence classified and covered up an investigation into a mutiny on the USS Pegasus, in order to conceal evidence of the testing of an illegal phasing cloaking device secretly developed by Starfleet Security. Twelve years later, Starfleet Intelligence, which had an operative in the Romulan High Command, learned that the Romulans were attempting to salvage the Pegasus. Erich Pressman, who was captain of the Pegasus at the time of the experiment, and who had subsequently been promoted to rear admiral and been attached to Starfleet Intelligence, boarded the USS Enterprise-D and mounted a mission to recover the Pegasus and the cloaking device before the Romulans. The Enterprise’s first officer, William T. Riker, who served under Pressman as an ensign on the Pegasus, eventually decided to inform Captain Picard of the development of the cloaking device, which was in direct violation of the Second Treaty Of Algeron which banned the use of such technology aboard Federation starships. Admiral Pressman was subsequently taken into custody, and Captain Picard surmised that the revelations of the conspiracy would lead to courts-martial of Pressman and several others in Starfleet Intelligence who were involved in the cover-up.
In 2369, Starfleet Intelligence came to believe that the Cardassians were developing a metagenic weapon on Celtris III. This spurred Starfleet to send Captain Picard, Doctor Beverly Crusher, and Lieutenant Worf on a covert mission to locate and destroy the weapon, but it was later revealed that the Cardassians had set a trap for the explicit purpose of capturing Captain Picard.
In 2370, Starfleet Intelligence provided the Enterprise with information concerning Arctus Baran’s Theta-class raider, which was conducting attacks against numerous archaeological sites in the Federation.
That same year, in an alternate timeline, Starfleet Intelligence learned of a massive deployment of Romulan vessels along the Neutral Zone, in response to a temporal anomaly discovered in the Devron system. In response, Admiral Nakamura ordered a fleet-wide yellow alert, and assigned the Enterprise and several other ships to respond to the Romulan deployment. The timeline in which these events occurred was later negated, and the events in question “unhappened,” when Captain Picard managed to prevent the formation of the anomaly from occurring.
Late in 2370, Benjamin Sisko had Starfleet Intelligence bring in suspected Maquis members for questioning to find out who could have been the recipient of a delivery of photon torpedo warheads stolen from Deep Space 9.
In 2371, Starfleet Intelligence prepared forged transit documents so that the USS Defiant could travel to Cardassia to rescue Major Kira Nerys.
In 2372, Intelligence believed that the Maquis were planning to hijack a shipment of industrial replicators that were bound for the war-ravaged Cardassian Union. It turned out that this information was accurate, but Intelligence failed to discover that there was a traitor working aboard Deep Space 9 – Michael Eddington. Eddington managed to make away with the entire shipment.
In early 2373, Intelligence discovered that Gowron had relocated Klingon military headquarters to Ty’Gokor.
Some time later that year, Starfleet Intelligence made some progress in breaking Maquis communication codes.
Another time later, Odo had Captain Sisko arrange a conference with Starfleet Intelligence via subspace. (DS9: “A Simple Investigation”) A short time later, Sisko told Kira that Intelligence would be extremely pleased about the information on Cardassian politics when she performed the shri-tal with Tekeny Ghemor.
Later that year, Sisko contacted Starfleet Intelligence to get confirmation that the Romulans had signed a non-aggression pact with the Dominion.
In 2375, Chakotay and Tuvok entered a restricted area of Terrasphere 8, Species 8472’s recreation of San Francisco. Ensign Gentry stopped and told them that all unauthorized personnel in the area had to be debriefed by Starfleet Intelligence under the orders of Admiral Bullock. Later, Bullock claimed that the reason why their Federation database contained no mention of Species 8472 was classified by Starfleet Intelligence.
During the Dominion War, Starfleet Intelligence was more powerful than ever, and played an important role in gathering information about the Dominion’s operations and infrastructure. One of its biggest coups was the location of a Dominion sensor array in early 2374, which the Dominion had been using to observe allied operations across five sectors of space.
During the breaking of the war, Starfleet Intelligence had a number of prominent agents. The chairman of the Romulan Tal Shiar Koval transferred valuable military intelligence and Glinn Lasaran from the Cardassian Union also served as an important agent.
One branch of Starfleet Intelligence was the Department of Internal Affairs, which was charged with keeping track of Starfleet operations to ensure that no security leaks occurred. In 2374, Luther Sloan posed as an agent of Internal Affairs while he was testing Julian Bashir in a fake holodeck scenario.
Also in 2374, Vice Admiral Fujisaki served as the Deputy Chief of Starfleet Intelligence, but died of “food poisoning” according to Sloan.
An undercover operation using Miles O’Brien infiltrating the Orion Syndicate on Farius Prime discovered it was colluding with the Dominion to arrange an assassination of a Klingon ambassador to damage the Federation-Klingon alliance. Chadwick of Starfleet Intelligence subsequently warned the Klingons and the attack was repulsed.
One of Intelligence’s greatest failures during the war was the neglect of the Dominion’s buildup in the Kalandra sector, from which the enemy launched a fleet to invade Betazed. The Dominion managed to capture the entire planet in under ten hours, because of the lack of warning. It would be one of the most humiliating defeats of the war.